Structure

Physi-Chem Properties

Molecular Weight:  228.07
Volume:  205.143
LogP:  -1.431
LogD:  -1.245
LogS:  -0.339
# Rotatable Bonds:  2
TPSA:  104.55
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.552
Synthetic Accessibility Score:  3.458
Fsp3:  0.556
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.885
MDCK Permeability:  0.00027360935928300023
Pgp-inhibitor:  0.001
Pgp-substrate:  0.017
Human Intestinal Absorption (HIA):  0.098
20% Bioavailability (F20%):  0.477
30% Bioavailability (F30%):  0.681

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.569
Plasma Protein Binding (PPB):  9.191762924194336%
Volume Distribution (VD):  0.569
Pgp-substrate:  79.61522674560547%

ADMET: Metabolism

CYP1A2-inhibitor:  0.01
CYP1A2-substrate:  0.16
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.053
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.212
CYP2D6-inhibitor:  0.008
CYP2D6-substrate:  0.099
CYP3A4-inhibitor:  0.004
CYP3A4-substrate:  0.069

ADMET: Excretion

Clearance (CL):  7.582
Half-life (T1/2):  0.823

ADMET: Toxicity

hERG Blockers:  0.011
Human Hepatotoxicity (H-HT):  0.943
Drug-inuced Liver Injury (DILI):  0.984
AMES Toxicity:  0.412
Rat Oral Acute Toxicity:  0.006
Maximum Recommended Daily Dose:  0.108
Skin Sensitization:  0.139
Carcinogencity:  0.149
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.019

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC106780

Natural Product ID:  NPC106780
Common Name*:   Deoxyuridine
IUPAC Name:   1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
Synonyms:   2'-Deoxyuridine; Deoxyuridine
Standard InCHIKey:  MXHRCPNRJAMMIM-SHYZEUOFSA-N
Standard InCHI:  InChI=1S/C9H12N2O5/c12-4-6-5(13)3-8(16-6)11-2-1-7(14)10-9(11)15/h1-2,5-6,8,12-13H,3-4H2,(H,10,14,15)/t5-,6+,8+/m0/s1
SMILES:  OC[C@H]1O[C@H](C[C@@H]1O)n1ccc(nc1=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL353955
PubChem CID:   13712
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000289] Nucleosides, nucleotides, and analogues
      • [CHEMONTID:0000480] Pyrimidine nucleosides
        • [CHEMONTID:0002180] Pyrimidine 2'-deoxyribonucleosides

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT189 Cell Line Vero Chlorocebus aethiops IC50 = 2.2 nM PMID[515840]
NPT1755 Individual Protein Thymidine kinase, cytosolic Homo sapiens ID50 = 400.0 uM PMID[515842]
NPT2868 Individual Protein Thymidine kinase 2 Rattus norvegicus Inhibition = 74.0 % PMID[515843]
NPT2869 Individual Protein Thymidine kinase Rattus norvegicus Inhibition = 90.0 % PMID[515843]
NPT3796 Individual Protein Thymidine kinase, cytosolic Mus musculus Activity = 93.0 % PMID[515844]
NPT3796 Individual Protein Thymidine kinase, cytosolic Mus musculus Activity = 65.0 % PMID[515844]
NPT4215 Individual Protein Deoxycytidine kinase Mus musculus Activity = 88.0 % PMID[515844]
NPT4215 Individual Protein Deoxycytidine kinase Mus musculus Activity = 92.0 % PMID[515844]
NPT3796 Individual Protein Thymidine kinase, cytosolic Mus musculus Relative phosphorylation = 0.55 n.a. PMID[515848]
NPT1755 Individual Protein Thymidine kinase, cytosolic Homo sapiens Relative phosphorylation = 1.0 n.a. PMID[515848]
NPT2873 Individual Protein Thymidine phosphorylase Escherichia coli K-12 Activity = 88.0 % PMID[515852]
NPT2873 Individual Protein Thymidine phosphorylase Escherichia coli K-12 Activity = 83.0 % PMID[515852]
NPT4216 Individual Protein Thymidine kinase, cytosolic Cricetulus griseus Inhibition = 38.0 % PMID[515856]
NPT4216 Individual Protein Thymidine kinase, cytosolic Cricetulus griseus Inhibition = 59.0 % PMID[515856]
NPT26550 SINGLE PROTEIN Thymidine phosphorylase Homo sapiens Km = 559000.0 nM PMID[515841]
NPT2 Others Unspecified Vmax = 0.88 uM min-1 PMID[515841]
NPT2 Others Unspecified Ki = 125000.0 nM PMID[515845]
NPT32 Organism Mus musculus Mus musculus Ki = 125000.0 nM PMID[515846]
NPT32 Organism Mus musculus Mus musculus Ki = 110000.0 nM PMID[515847]
NPT32 Organism Mus musculus Mus musculus Ki = 130000.0 nM PMID[515849]
NPT32 Organism Mus musculus Mus musculus Ki = 0.11 n.a. PMID[515850]
NPT27 Others Unspecified CC50 > 200.0 ug.mL-1 PMID[515855]
NPT963 Organism Hepatitis B virus Hepatitis B virus Inhibition = 0.0 % PMID[515855]
NPT2 Others Unspecified Ki = 290000.0 nM PMID[515857]
NPT2 Others Unspecified Ki = 9500.0 nM PMID[515858]
NPT35 Others n.a. pKa = 9.3 n.a. PMID[515858]
NPT1531 Organism Enterococcus faecium Enterococcus faecium ED50 = 37.0 uM PMID[515858]
NPT26861 SINGLE PROTEIN Bifunctional dihydrofolate reductase-thymidylate synthase Cryptosporidium hominis Inhibition = -5.3 % PMID[515859]

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC106780 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.962 High Similarity NPC43246
0.962 High Similarity NPC89051
0.9157 High Similarity NPC324390
0.9048 High Similarity NPC322594
0.9048 High Similarity NPC320249
0.8889 High Similarity NPC71339
0.8889 High Similarity NPC112842
0.8837 High Similarity NPC17892
0.8837 High Similarity NPC36985
0.881 High Similarity NPC315063
0.8736 High Similarity NPC73765
0.8736 High Similarity NPC283698
0.8571 High Similarity NPC210456
0.8571 High Similarity NPC163352
0.8372 Intermediate Similarity NPC171116
0.8182 Intermediate Similarity NPC327344
0.8025 Intermediate Similarity NPC329077
0.8 Intermediate Similarity NPC229249
0.8 Intermediate Similarity NPC324516
0.8 Intermediate Similarity NPC318166
0.7927 Intermediate Similarity NPC325902
0.7912 Intermediate Similarity NPC317639
0.7835 Intermediate Similarity NPC329277
0.7727 Intermediate Similarity NPC62927
0.7727 Intermediate Similarity NPC190334
0.7677 Intermediate Similarity NPC149843
0.7677 Intermediate Similarity NPC155087
0.7356 Intermediate Similarity NPC319753
0.7303 Intermediate Similarity NPC325723
0.7234 Intermediate Similarity NPC329384
0.7158 Intermediate Similarity NPC226769
0.7158 Intermediate Similarity NPC280946
0.7158 Intermediate Similarity NPC6166
0.7083 Intermediate Similarity NPC90240
0.7083 Intermediate Similarity NPC120887
0.701 Intermediate Similarity NPC328779
0.6882 Remote Similarity NPC328806
0.6869 Remote Similarity NPC328914
0.6667 Remote Similarity NPC284651
0.6628 Remote Similarity NPC315806
0.6609 Remote Similarity NPC315058
0.6441 Remote Similarity NPC313962
0.6422 Remote Similarity NPC478024
0.6289 Remote Similarity NPC109188
0.6154 Remote Similarity NPC325750
0.5761 Remote Similarity NPC470782
0.5714 Remote Similarity NPC126186
0.569 Remote Similarity NPC313813
0.5652 Remote Similarity NPC192521
0.5641 Remote Similarity NPC224624
0.561 Remote Similarity NPC293551

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC106780 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.9744 High Similarity NPD9557 Clinical (unspecified phase)
0.962 High Similarity NPD9580 Clinical (unspecified phase)
0.962 High Similarity NPD9581 Clinical (unspecified phase)
0.9231 High Similarity NPD9556 Approved
0.9114 High Similarity NPD9560 Approved
0.9114 High Similarity NPD9561 Approved
0.9 High Similarity NPD9546 Phase 2
0.8929 High Similarity NPD9565 Discontinued
0.8889 High Similarity NPD280 Approved
0.8889 High Similarity NPD9533 Phase 2
0.8736 High Similarity NPD9639 Clinical (unspecified phase)
0.8675 High Similarity NPD240 Phase 3
0.8675 High Similarity NPD170 Approved
0.8675 High Similarity NPD9562 Discovery
0.8537 High Similarity NPD9529 Phase 1
0.8537 High Similarity NPD9559 Phase 1
0.8519 High Similarity NPD9558 Phase 3
0.8434 Intermediate Similarity NPD239 Phase 2
0.8434 Intermediate Similarity NPD238 Clinical (unspecified phase)
0.8409 Intermediate Similarity NPD501 Phase 1
0.8372 Intermediate Similarity NPD841 Approved
0.8372 Intermediate Similarity NPD755 Phase 3
0.8295 Intermediate Similarity NPD1686 Approved
0.8222 Intermediate Similarity NPD762 Discontinued
0.814 Intermediate Similarity NPD241 Discontinued
0.8132 Intermediate Similarity NPD502 Approved
0.8 Intermediate Similarity NPD9601 Approved
0.7978 Intermediate Similarity NPD251 Approved
0.7835 Intermediate Similarity NPD3129 Phase 3
0.7732 Intermediate Similarity NPD3128 Phase 3
0.7727 Intermediate Similarity NPD9604 Approved
0.7727 Intermediate Similarity NPD9602 Phase 3
0.7727 Intermediate Similarity NPD9603 Phase 3
0.766 Intermediate Similarity NPD5789 Clinical (unspecified phase)
0.7647 Intermediate Similarity NPD9600 Approved
0.764 Intermediate Similarity NPD9553 Approved
0.764 Intermediate Similarity NPD9554 Approved
0.7528 Intermediate Similarity NPD1760 Approved
0.7526 Intermediate Similarity NPD1061 Clinical (unspecified phase)
0.7473 Intermediate Similarity NPD267 Discontinued
0.7471 Intermediate Similarity NPD9572 Clinical (unspecified phase)
0.7444 Intermediate Similarity NPD301 Discontinued
0.7391 Intermediate Similarity NPD6943 Clinical (unspecified phase)
0.7391 Intermediate Similarity NPD9585 Discontinued
0.7356 Intermediate Similarity NPD9573 Phase 2
0.7292 Intermediate Similarity NPD192 Phase 2
0.7234 Intermediate Similarity NPD215 Discontinued
0.7216 Intermediate Similarity NPD223 Clinical (unspecified phase)
0.7179 Intermediate Similarity NPD9503 Approved
0.7179 Intermediate Similarity NPD9504 Approved
0.717 Intermediate Similarity NPD3139 Phase 3
0.7129 Intermediate Similarity NPD1385 Discontinued
0.7111 Intermediate Similarity NPD9555 Phase 2
0.7097 Intermediate Similarity NPD500 Discontinued
0.7083 Intermediate Similarity NPD514 Clinical (unspecified phase)
0.7075 Intermediate Similarity NPD3138 Phase 3
0.7071 Intermediate Similarity NPD7651 Approved
0.6947 Remote Similarity NPD279 Clinical (unspecified phase)
0.6931 Remote Similarity NPD2633 Phase 1
0.6869 Remote Similarity NPD1454 Phase 3
0.6869 Remote Similarity NPD1455 Phase 3
0.6778 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6729 Remote Similarity NPD7914 Suspended
0.6706 Remote Similarity NPD9405 Approved
0.6667 Remote Similarity NPD6693 Phase 3
0.6635 Remote Similarity NPD1428 Phase 2
0.663 Remote Similarity NPD205 Approved
0.6628 Remote Similarity NPD9653 Clinical (unspecified phase)
0.66 Remote Similarity NPD3121 Phase 2
0.6556 Remote Similarity NPD9429 Discontinued
0.6538 Remote Similarity NPD6946 Approved
0.6535 Remote Similarity NPD765 Discontinued
0.6477 Remote Similarity NPD9407 Approved
0.6389 Remote Similarity NPD1804 Phase 2
0.6389 Remote Similarity NPD1805 Phase 2
0.6327 Remote Similarity NPD285 Discontinued
0.6289 Remote Similarity NPD1331 Approved
0.6286 Remote Similarity NPD4743 Phase 2
0.6283 Remote Similarity NPD7756 Clinical (unspecified phase)
0.6186 Remote Similarity NPD723 Phase 2
0.6053 Remote Similarity NPD7992 Clinical (unspecified phase)
0.6053 Remote Similarity NPD6935 Phase 3
0.6053 Remote Similarity NPD6936 Clinical (unspecified phase)
0.604 Remote Similarity NPD1706 Clinical (unspecified phase)
0.6 Remote Similarity NPD6918 Phase 1
0.5938 Remote Similarity NPD7761 Suspended
0.5888 Remote Similarity NPD244 Clinical (unspecified phase)
0.5769 Remote Similarity NPD2621 Clinical (unspecified phase)
0.5745 Remote Similarity NPD9427 Approved
0.5673 Remote Similarity NPD6948 Phase 3
0.5638 Remote Similarity NPD9372 Phase 2

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data